Aims:  Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results:  Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions:  The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study:  The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial proteins, short chain fatty acids and gases. In this study, metagenomic approaches were used to study the microbial populations and metabolic potential of the microbial community. DNA was extracted from Surti Buffalo rumen samples (four treatments diet) and sequenced separately using a 454 GS FLX Titanium system. We used comparative metagenomics to examine metabolic potential and phylogenetic composition from pyrosequence data generated in four samples, considering phylogenetic composition and metabolic potentials in the rumen may remarkably be different with respect to nutrient utilization. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of fermentation of carbohydrates in a high roughage diet. The distribution of phylotypes and environmental gene tags (EGTs) detected within each rumen sample were dominated by Bacteroidetes/Chlorobi, Firmicutes and Proteobacteria in all the samples. The results of this study could help to determine the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals.

Lactobacillus helveticus MTCC 5463 was isolated from a vaginal swab from a healthy adult female. The strain exhibited potential probiotic properties, with their beneficial role in the gastrointestinal tract and their ability to reduce cholesterol and stimulate immunity. We sequenced the whole genome and compared it with the published genome sequence of Lactobacillus helveticus DPC4571.Lactobacillus helveticus is present in fermented foods and is also used as a probiotic (4,10,12). Researchers have evaluated the effect of L. helveticus against diseases such as cancer and intestinal inflammation. Milk fermented with L. helveticus R389 delayed breast tumor growth by decreasing interleukin-6 (IL-6) and increasing IL-10 in serum, mammary glands, and tumor-infiltrating immune cells (5). Lactobacillus helveticus strains are normally isolated from milk products and intestinal microflora (6,14). The L. helveticus MTCC 5463 strain was originally isolated from the vaginal tract of a healthy adult female in India at Anand Agricultural University (9). The L. helveticus MTCC 5463 strain, earlier known as Lactobacillus acidophilus V3 (based on biochemical characteristics) was able to grow in the presence of 0.3% sodium taurocholate, deconjugate bile acids, and reduce cholesterol in vitro (1). The strain exhibited significant antimicrobial activity against Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica serovar Typhi, and Escherichia coli (7). The strain produced extracellular polysaccharide and was able to adhere to cells of the human carcinoma cell line HT29. A hypocholesterolemic effect of L. helveticus MTCC 5463 was reported in human subjects with different cholesterol levels (2). The strain has also shown positive immunomodulating effects in a chick model (13).The whole-genome sequencing of L. helveticus MTCC 5463 was performed using GS-FLX Titanium reagents (11). The data generated from the genomic library contained 119,569 reads, and assembly generated a 1,911,350-bp single chromosome. The genome annotation and comparative analysis of the genome were done with the published genome of strain DPC4571 (3). The genomic sequence of L. helveticus MTCC 5463 was somewhat smaller than those of L. helveticus DPC4571 (2.08 Mb) and L. helveticus H10 (2.14 Mb). In total, 2,046 coding sequence (CDS) regions and 71 RNA genes were reported. Of the 71 RNA genes, 59 coded for tRNA, 8 for rRNA, and 4 for 5S RNA. The CDS regions were slightly fewer than in L. helveticus H10 (2,049) and L. helveticus DPC4571 (2,238). Metabolic reconstruction subsystems were assembled to create a metabolic reaction network for L. helveticus MTCC 5463 and L. helveticus DPC4571.The subsystem analysis revealed a common subsystem structure between L. helveticus MTCC 5463 and L. helveticus DPC4571 for seven subsystems, viz., photosynthesis, iron acquisition and metabolism, motility and chemotaxis, secondary metabolism, stress response, nitrogen metabolism, and dormancy and sporulation. The considerable variation observed in the ...

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